Code Monkey home page Code Monkey logo

aaszodi / multovl Goto Github PK

View Code? Open in Web Editor NEW
2.0 1.0 0.0 2.84 MB

Very fast and efficient detection of multiple overlaps between genomic regions. For details on the algorithm and the implementation, please refer to the following publication: Aszódi, A. (2012): MULTOVL: Fast multiple overlaps of genomic regions. Bioinformatics 28: 3318-3319.

License: Other

CMake 7.73% C 1.77% C++ 88.69% Shell 1.60% Awk 0.17% Dockerfile 0.05%
genomic-regions bioinformatics-algorithms

multovl's Introduction

Multiple Overlap of Genomic Regions

by András Aszódi

Version 1.4

This program is licensed under the terms of the BSD Open Source license. See the file LICENSE for details.

Pre-compiled binaries are provided for some popular architectures. If you want to build Multovl from scratch, keep on reading:

Building instructions

See doc/html/guide.html for installation instructions and a detailed documentation.

Prerequisites

You will need cmake Version 3.1 or above, a C++11-compliant compiler, and the Boost libraries (1.74 or above) to build Multovl.

For the very impatient

Run the quickbuild.sh script in the top-level Multovl directory. This will compile the package using static linkage, assuming a Linux platform, Boost libraries installed in the usual system location. You have to specify the installation prefix by providing a path as a command line argument. E.g. quickbuild.sh $HOME/foo/bar will install the Multovl executables into $HOME/foo/bar/multovl-1.4/bin.

For the moderately impatient

By default all these external libraries will be linked statically. To link all of them dynamically instead, specify the CMake option -DMULTOVL_USE_DYNAMIC_LIBS:BOOL=ON

The basic steps if you use the default system compilers:

mkdir build 
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DBOOST_ROOT=/path/to/boost \
    -DCMAKE_INSTALL_PREFIX=/path/to/installdir ..
make

Or you can spell out what make all does:

make apps
make doc    # this generates Doxygen documentation if you have Doxygen installed

And then finally:

make install (this you may need to run as root, depending on installdir permissions)

The tools should now be installed in ${CMAKE_INSTALL_PREFIX}/multovl-1.3/bin.

Additional Cmake settings are listed in the top-level CMakeLists.txt, or you may run cmake -i for interactive options, or ccmake.

multovl's People

Contributors

aaszodi avatar bookest avatar chmille4 avatar ekg avatar gaberudy avatar grenaud avatar leecbaker avatar pezmaster31 avatar

Stargazers

 avatar  avatar

Watchers

 avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.